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Research Project: Discovery of Plant Genetic Mechanisms Controlling Microbial Recruitment to the Root Microbiome

Location: Plant Gene Expression Center

Title: A plant growth-promoting microbial soil amendment dynamically alters the strawberry root bacterial microbiome

item DENG, SIWEN - University Of California
item WIPF, HEIDI - University Of California
item PIERROZ, GRADY - University Of California
item RAAB, TED - Stanford University
item KHANNA, RAJNISH - I-Cultiver
item Coleman-Derr, Devin

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/1/2019
Publication Date: 11/27/2019
Citation: Deng, S., Wipf, H., Pierroz, G., Raab, T.K., Khanna, R., Coleman-Derr, D.A. 2019. A plant growth-promoting microbial soil amendment dynamically alters the strawberry root bacterial microbiome. Scientific Reports. 9:17677.

Interpretive Summary: In this study, we explore the effect of a commercially available microbial soil amendment, VESTA, on the microbiome of strawberries, an important horticultural crop. Strawberries are valued at US$2.8 billion nationally and face a number of stress-related challenges. Past work has shown that its growth can be regulated by microbial means. Gene amplicon-based metagenomics approaches have identified microbes that potentially play a role in yield decline in strawberry, where low abundances of beneficial bacteria and a nematode fungus, in addition to high levels of fungal root rot pathogens, were implicated. Taken together, these recent findings suggest that manipulating the strawberry microbiome may be an effective way to increase plant growth.

Technical Abstract: Despite growing interest in utilizing microbial-based methods for improving crop growth, much work still remains in elucidating how beneficial plant-microbe associations are established, and what role soil amendments play in shaping these interactions. Here, we describe a set of experiments that test the effect of a commercially available soil amendment, VESTA, on the soil and strawberry (Fragaria x ananassa Monterey) root bacterial microbiome. The bacterial communities of the soil, rhizosphere, and root from amendment-treated and untreated fields were profiled at four time points across the strawberry growing season using 16S rRNA gene amplicon sequencing on the Illumina MiSeq platform. In all sample types, bacterial community composition and relative abundance were significantly altered with amendment application. Importantly, time point effects on composition are more pronounced in the root and rhizosphere, suggesting an interaction between plant development and treatment effect. Surprisingly, there was slight overlap between the taxa within the amendment and those enriched in plant and soil following treatment, suggesting that VESTA may act to rewire existing networks of organisms through an, as of yet, uncharacterized mechanism. These findings demonstrate that a commercial microbial soil amendment can impact the bacterial community structure of both roots and the surrounding environment